[BioC] zebrafish simpleaffy Error in FUN(X[[4]], ...) : subscript out of bounds

[Crispin Miller]

Hi,
This is interesting... I've tried to duplicate this with 2.1.3 from the
devel library and the current release version and it works fine for me
on windows and on linux. Please can you try updating to 2.1.3 and seeing
if that fixes things? 
If not then let me know and we can try to explore things further.
Best,

Crispin
 

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Dick Beyer
Sent: 27 July 2005 00:33
To: Bioconductor
Subject: [BioC] zebrafish simpleaffy Error in FUN(X[[4]], ...) :
subscript out of bounds

I have a problem with simpleaffy and zebrafish:

> all.raw
AffyBatch object
size of arrays=712x712 features (11889 kb) cdf=Zebrafish (15617 affyids)
number of samples=3 number of genes=15617 annotation=zebrafish

> all.mas5 <- call.exprs(all.raw,"mas5")
Background correcting
Retrieving data from AffyBatch...done.
Computing expression calls... 
...done.
scaling to a TGT of 100 ...
Scale factor for: EG Zebrafish control 20July05.CEL 1.07236539803815
Scale factor for: EG Zebrafish 310 20July05.CEL 1.14945565186904 Scale
factor for: EG Zebrafish 820 20July05.CEL 1.04463357372716 
> qc <- qc(all.raw,all.mas5)
Getting probe level data...
Computing p-values
Doing PMA Calls
Error in FUN(X[[4]], ...) : subscript out of bounds

> sessionInfo()
R version 2.1.1, 2005-07-10, i386-pc-mingw32

attached base packages:
[1] "tools"     "methods"   "stats"     "graphics"  "grDevices"
[6] "utils"     "datasets"  "base"

other attached packages:
zebrafishprobe   zebrafishcdf      zebrafish         qvalue
          "1.1"        "1.5.1"        "1.8.4"          "1.1"
          gcrma    matchprobes     simpleaffy           affy
        "1.1.4"       "1.0.22"        "2.1.1"        "1.6.7"
     reposTools        Biobase
       "1.5.19"       "1.5.12"

Thanks very much,
Dick

************************************************************************
*******
Richard P. Beyer, Ph.D.	University of Washington
Tel.:(206) 616 7378	Env. & Occ. Health Sci. , Box 354695
Fax: (206) 685 4696	4225 Roosevelt Way NE, # 100
 			Seattle, WA 98105-6099
http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html
http://staff.washington.edu/~dbeyer

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